Per chromosome imputation report for cohort Group3.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 31.5.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 12595817 | 73.058 |
| 0.1 | 1226219 | 7.112 |
| 0.2 | 808584 | 4.690 |
| 0.3 | 620241 | 3.597 |
| 0.4 | 497181 | 2.884 |
| 0.5 | 405055 | 2.349 |
| 0.6 | 349175 | 2.025 |
| 0.7 | 293852 | 1.704 |
| 0.8 | 243313 | 1.411 |
| 0.9 | 201520 | 1.169 |
| Total | 17240957 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 561146 | 3.255 |
| 0.4 | 551448 | 3.198 |
| 0.5 | 605396 | 3.511 |
| 0.6 | 913161 | 5.296 |
| 0.7 | 1583194 | 9.183 |
| 0.8 | 2726243 | 15.813 |
| 0.9 | 10273304 | 59.587 |
| 1.0 | 27065 | 0.157 |
| Total | 17240957 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 952070 | 73.3742 |
| 0.1 | 90296 | 6.9589 |
| 0.2 | 57511 | 4.4323 |
| 0.3 | 45806 | 3.5302 |
| 0.4 | 36970 | 2.8492 |
| 0.5 | 30766 | 2.3711 |
| 0.6 | 27010 | 2.0816 |
| 0.7 | 22246 | 1.7145 |
| 0.8 | 18491 | 1.4251 |
| 0.9 | 16389 | 1.2631 |
| Total | 1297555 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 43902 | 3.3834 |
| 0.4 | 43081 | 3.3202 |
| 0.5 | 46163 | 3.5577 |
| 0.6 | 68122 | 5.2500 |
| 0.7 | 118899 | 9.1633 |
| 0.8 | 208119 | 16.0393 |
| 0.9 | 767755 | 59.1694 |
| 1.0 | 1514 | 0.1167 |
| Total | 1297555 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1061194 | 73.7986 |
| 0.1 | 100934 | 7.0192 |
| 0.2 | 66190 | 4.6030 |
| 0.3 | 49257 | 3.4255 |
| 0.4 | 38553 | 2.6811 |
| 0.5 | 32766 | 2.2786 |
| 0.6 | 28615 | 1.9900 |
| 0.7 | 23482 | 1.6330 |
| 0.8 | 20138 | 1.4005 |
| 0.9 | 16831 | 1.1705 |
| Total | 1437960 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 46664 | 3.2452 |
| 0.4 | 44404 | 3.0880 |
| 0.5 | 48259 | 3.3561 |
| 0.6 | 73693 | 5.1248 |
| 0.7 | 129874 | 9.0318 |
| 0.8 | 230448 | 16.0260 |
| 0.9 | 862867 | 60.0063 |
| 1.0 | 1751 | 0.1218 |
| Total | 1437960 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 893321 | 73.3088 |
| 0.1 | 87404 | 7.1727 |
| 0.2 | 55484 | 4.5532 |
| 0.3 | 42770 | 3.5098 |
| 0.4 | 35788 | 2.9369 |
| 0.5 | 28640 | 2.3503 |
| 0.6 | 24740 | 2.0302 |
| 0.7 | 20378 | 1.6723 |
| 0.8 | 17000 | 1.3951 |
| 0.9 | 13047 | 1.0707 |
| Total | 1218572 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 37840 | 3.1053 |
| 0.4 | 36976 | 3.0344 |
| 0.5 | 39145 | 3.2124 |
| 0.6 | 60053 | 4.9281 |
| 0.7 | 107120 | 8.7906 |
| 0.8 | 193716 | 15.8970 |
| 0.9 | 741817 | 60.8759 |
| 1.0 | 1905 | 0.1563 |
| Total | 1218572 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 856320 | 71.9719 |
| 0.1 | 82859 | 6.9641 |
| 0.2 | 60861 | 5.1152 |
| 0.3 | 45157 | 3.7954 |
| 0.4 | 34261 | 2.8796 |
| 0.5 | 27608 | 2.3204 |
| 0.6 | 24437 | 2.0539 |
| 0.7 | 22094 | 1.8570 |
| 0.8 | 19785 | 1.6629 |
| 0.9 | 16415 | 1.3796 |
| Total | 1189797 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 37810 | 3.1779 |
| 0.4 | 36914 | 3.1025 |
| 0.5 | 39964 | 3.3589 |
| 0.6 | 59493 | 5.0003 |
| 0.7 | 105663 | 8.8808 |
| 0.8 | 185664 | 15.6047 |
| 0.9 | 723058 | 60.7715 |
| 1.0 | 1231 | 0.1035 |
| Total | 1189797 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 808850 | 73.3415 |
| 0.1 | 77360 | 7.0145 |
| 0.2 | 52426 | 4.7537 |
| 0.3 | 40314 | 3.6554 |
| 0.4 | 31538 | 2.8597 |
| 0.5 | 24209 | 2.1951 |
| 0.6 | 23148 | 2.0989 |
| 0.7 | 18261 | 1.6558 |
| 0.8 | 14898 | 1.3509 |
| 0.9 | 11851 | 1.0746 |
| Total | 1102855 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 34681 | 3.1447 |
| 0.4 | 33593 | 3.0460 |
| 0.5 | 36189 | 3.2814 |
| 0.6 | 55164 | 5.0019 |
| 0.7 | 97229 | 8.8161 |
| 0.8 | 172857 | 15.6736 |
| 0.9 | 671746 | 60.9097 |
| 1.0 | 1396 | 0.1266 |
| Total | 1102855 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 783815 | 72.3661 |
| 0.1 | 79982 | 7.3844 |
| 0.2 | 53044 | 4.8973 |
| 0.3 | 41061 | 3.7910 |
| 0.4 | 32608 | 3.0105 |
| 0.5 | 26451 | 2.4421 |
| 0.6 | 21988 | 2.0301 |
| 0.7 | 17501 | 1.6158 |
| 0.8 | 15269 | 1.4097 |
| 0.9 | 11406 | 1.0531 |
| Total | 1083125 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 32224 | 2.9751 |
| 0.4 | 31800 | 2.9359 |
| 0.5 | 34548 | 3.1897 |
| 0.6 | 50868 | 4.6964 |
| 0.7 | 89283 | 8.2431 |
| 0.8 | 160140 | 14.7850 |
| 0.9 | 677249 | 62.5273 |
| 1.0 | 7013 | 0.6475 |
| Total | 1083125 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 701088 | 72.6673 |
| 0.1 | 69085 | 7.1606 |
| 0.2 | 48053 | 4.9807 |
| 0.3 | 35763 | 3.7068 |
| 0.4 | 28942 | 2.9998 |
| 0.5 | 23261 | 2.4110 |
| 0.6 | 19280 | 1.9984 |
| 0.7 | 16554 | 1.7158 |
| 0.8 | 11929 | 1.2364 |
| 0.9 | 10837 | 1.1232 |
| Total | 964792 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 31238 | 3.2378 |
| 0.4 | 30318 | 3.1424 |
| 0.5 | 33144 | 3.4354 |
| 0.6 | 49818 | 5.1636 |
| 0.7 | 87033 | 9.0209 |
| 0.8 | 149827 | 15.5295 |
| 0.9 | 582043 | 60.3283 |
| 1.0 | 1371 | 0.1421 |
| Total | 964792 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 707357 | 73.9793 |
| 0.1 | 64852 | 6.7826 |
| 0.2 | 43730 | 4.5735 |
| 0.3 | 32685 | 3.4184 |
| 0.4 | 27580 | 2.8845 |
| 0.5 | 21377 | 2.2357 |
| 0.6 | 19512 | 2.0407 |
| 0.7 | 15419 | 1.6126 |
| 0.8 | 13091 | 1.3691 |
| 0.9 | 10552 | 1.1036 |
| Total | 956155 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 29802 | 3.1169 |
| 0.4 | 29582 | 3.0938 |
| 0.5 | 32711 | 3.4211 |
| 0.6 | 48336 | 5.0552 |
| 0.7 | 85032 | 8.8931 |
| 0.8 | 151981 | 15.8950 |
| 0.9 | 577344 | 60.3818 |
| 1.0 | 1367 | 0.1430 |
| Total | 956155 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 528874 | 73.1207 |
| 0.1 | 54463 | 7.5299 |
| 0.2 | 33701 | 4.6594 |
| 0.3 | 25073 | 3.4665 |
| 0.4 | 20598 | 2.8478 |
| 0.5 | 15719 | 2.1733 |
| 0.6 | 14483 | 2.0024 |
| 0.7 | 11939 | 1.6507 |
| 0.8 | 9644 | 1.3334 |
| 0.9 | 8795 | 1.2160 |
| Total | 723289 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 23237 | 3.2127 |
| 0.4 | 22937 | 3.1712 |
| 0.5 | 25199 | 3.4839 |
| 0.6 | 38708 | 5.3517 |
| 0.7 | 66675 | 9.2183 |
| 0.8 | 116885 | 16.1602 |
| 0.9 | 428770 | 59.2806 |
| 1.0 | 878 | 0.1214 |
| Total | 723289 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 606853 | 72.6499 |
| 0.1 | 60660 | 7.2620 |
| 0.2 | 40141 | 4.8055 |
| 0.3 | 28161 | 3.3713 |
| 0.4 | 25200 | 3.0168 |
| 0.5 | 20472 | 2.4508 |
| 0.6 | 17289 | 2.0698 |
| 0.7 | 14335 | 1.7161 |
| 0.8 | 12521 | 1.4990 |
| 0.9 | 9680 | 1.1588 |
| Total | 835312 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 27313 | 3.2698 |
| 0.4 | 27084 | 3.2424 |
| 0.5 | 27627 | 3.3074 |
| 0.6 | 41647 | 4.9858 |
| 0.7 | 73713 | 8.8246 |
| 0.8 | 128009 | 15.3247 |
| 0.9 | 508906 | 60.9241 |
| 1.0 | 1013 | 0.1213 |
| Total | 835312 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 595701 | 72.4771 |
| 0.1 | 58607 | 7.1305 |
| 0.2 | 36207 | 4.4052 |
| 0.3 | 31124 | 3.7868 |
| 0.4 | 24017 | 2.9221 |
| 0.5 | 20888 | 2.5414 |
| 0.6 | 17741 | 2.1585 |
| 0.7 | 14378 | 1.7493 |
| 0.8 | 12351 | 1.5027 |
| 0.9 | 10902 | 1.3264 |
| Total | 821916 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25751 | 3.1330 |
| 0.4 | 25134 | 3.0580 |
| 0.5 | 27553 | 3.3523 |
| 0.6 | 41856 | 5.0925 |
| 0.7 | 73703 | 8.9672 |
| 0.8 | 128199 | 15.5976 |
| 0.9 | 498474 | 60.6478 |
| 1.0 | 1246 | 0.1516 |
| Total | 821916 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 580494 | 72.8946 |
| 0.1 | 57064 | 7.1657 |
| 0.2 | 35767 | 4.4914 |
| 0.3 | 30109 | 3.7809 |
| 0.4 | 23105 | 2.9014 |
| 0.5 | 19057 | 2.3931 |
| 0.6 | 15735 | 1.9759 |
| 0.7 | 13018 | 1.6347 |
| 0.8 | 12331 | 1.5484 |
| 0.9 | 9667 | 1.2139 |
| Total | 796347 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25246 | 3.1702 |
| 0.4 | 24896 | 3.1263 |
| 0.5 | 26772 | 3.3619 |
| 0.6 | 40052 | 5.0295 |
| 0.7 | 72049 | 9.0474 |
| 0.8 | 124604 | 15.6469 |
| 0.9 | 481487 | 60.4620 |
| 1.0 | 1241 | 0.1558 |
| Total | 796347 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 422367 | 71.2972 |
| 0.1 | 43623 | 7.3637 |
| 0.2 | 27692 | 4.6745 |
| 0.3 | 22983 | 3.8796 |
| 0.4 | 17481 | 2.9509 |
| 0.5 | 15658 | 2.6431 |
| 0.6 | 12518 | 2.1131 |
| 0.7 | 11202 | 1.8909 |
| 0.8 | 9834 | 1.6600 |
| 0.9 | 9045 | 1.5268 |
| Total | 592403 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 18136 | 3.0614 |
| 0.4 | 18038 | 3.0449 |
| 0.5 | 19638 | 3.3150 |
| 0.6 | 30286 | 5.1124 |
| 0.7 | 54155 | 9.1416 |
| 0.8 | 93421 | 15.7698 |
| 0.9 | 358335 | 60.4884 |
| 1.0 | 394 | 0.0665 |
| Total | 592403 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 395998 | 72.9954 |
| 0.1 | 40120 | 7.3954 |
| 0.2 | 26136 | 4.8177 |
| 0.3 | 18615 | 3.4314 |
| 0.4 | 15451 | 2.8481 |
| 0.5 | 12184 | 2.2459 |
| 0.6 | 9915 | 1.8277 |
| 0.7 | 9381 | 1.7292 |
| 0.8 | 7763 | 1.4310 |
| 0.9 | 6934 | 1.2782 |
| Total | 542497 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17506 | 3.2269 |
| 0.4 | 17089 | 3.1501 |
| 0.5 | 18473 | 3.4052 |
| 0.6 | 28449 | 5.2441 |
| 0.7 | 49685 | 9.1586 |
| 0.8 | 84476 | 15.5717 |
| 0.9 | 326141 | 60.1185 |
| 1.0 | 678 | 0.1250 |
| Total | 542497 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 339363 | 72.6854 |
| 0.1 | 33056 | 7.0800 |
| 0.2 | 21803 | 4.6698 |
| 0.3 | 16910 | 3.6218 |
| 0.4 | 14363 | 3.0763 |
| 0.5 | 11616 | 2.4879 |
| 0.6 | 8867 | 1.8992 |
| 0.7 | 7837 | 1.6785 |
| 0.8 | 6479 | 1.3877 |
| 0.9 | 6599 | 1.4134 |
| Total | 466893 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 15817 | 3.3877 |
| 0.4 | 15141 | 3.2429 |
| 0.5 | 17327 | 3.7111 |
| 0.6 | 25826 | 5.5315 |
| 0.7 | 44178 | 9.4621 |
| 0.8 | 74321 | 15.9182 |
| 0.9 | 273850 | 58.6537 |
| 1.0 | 433 | 0.0927 |
| Total | 466893 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 395103 | 74.0757 |
| 0.1 | 37742 | 7.0760 |
| 0.2 | 23073 | 4.3258 |
| 0.3 | 18918 | 3.5468 |
| 0.4 | 14203 | 2.6628 |
| 0.5 | 12136 | 2.2753 |
| 0.6 | 10739 | 2.0134 |
| 0.7 | 9402 | 1.7627 |
| 0.8 | 6835 | 1.2815 |
| 0.9 | 5226 | 0.9798 |
| Total | 533377 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 19104 | 3.5817 |
| 0.4 | 19031 | 3.5680 |
| 0.5 | 21464 | 4.0242 |
| 0.6 | 31130 | 5.8364 |
| 0.7 | 52178 | 9.7826 |
| 0.8 | 86962 | 16.3040 |
| 0.9 | 303082 | 56.8232 |
| 1.0 | 426 | 0.0799 |
| Total | 533377 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 338374 | 73.7251 |
| 0.1 | 30352 | 6.6131 |
| 0.2 | 23063 | 5.0250 |
| 0.3 | 15204 | 3.3127 |
| 0.4 | 13645 | 2.9730 |
| 0.5 | 11104 | 2.4193 |
| 0.6 | 8937 | 1.9472 |
| 0.7 | 8252 | 1.7980 |
| 0.8 | 5829 | 1.2700 |
| 0.9 | 4207 | 0.9166 |
| Total | 458967 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 16912 | 3.6848 |
| 0.4 | 16656 | 3.6290 |
| 0.5 | 19045 | 4.1495 |
| 0.6 | 28670 | 6.2466 |
| 0.7 | 47529 | 10.3556 |
| 0.8 | 75054 | 16.3528 |
| 0.9 | 254337 | 55.4151 |
| 1.0 | 764 | 0.1665 |
| Total | 458967 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 344192 | 72.5219 |
| 0.1 | 34108 | 7.1866 |
| 0.2 | 23332 | 4.9161 |
| 0.3 | 17755 | 3.7410 |
| 0.4 | 13983 | 2.9462 |
| 0.5 | 11062 | 2.3308 |
| 0.6 | 9103 | 1.9180 |
| 0.7 | 8273 | 1.7431 |
| 0.8 | 6602 | 1.3911 |
| 0.9 | 6194 | 1.3051 |
| Total | 474604 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 15100 | 3.1816 |
| 0.4 | 14736 | 3.1049 |
| 0.5 | 16602 | 3.4981 |
| 0.6 | 26128 | 5.5052 |
| 0.7 | 44826 | 9.4449 |
| 0.8 | 76700 | 16.1608 |
| 0.9 | 280187 | 59.0360 |
| 1.0 | 325 | 0.0685 |
| Total | 474604 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 263942 | 72.2824 |
| 0.1 | 29529 | 8.0867 |
| 0.2 | 18438 | 5.0494 |
| 0.3 | 13479 | 3.6913 |
| 0.4 | 9785 | 2.6797 |
| 0.5 | 8582 | 2.3502 |
| 0.6 | 6918 | 1.8945 |
| 0.7 | 6360 | 1.7417 |
| 0.8 | 4480 | 1.2269 |
| 0.9 | 3641 | 0.9971 |
| Total | 365154 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 12957 | 3.5484 |
| 0.4 | 13173 | 3.6075 |
| 0.5 | 14713 | 4.0293 |
| 0.6 | 23187 | 6.3499 |
| 0.7 | 37837 | 10.3619 |
| 0.8 | 58530 | 16.0289 |
| 0.9 | 203915 | 55.8436 |
| 1.0 | 842 | 0.2306 |
| Total | 365154 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 271018 | 72.8537 |
| 0.1 | 27448 | 7.3784 |
| 0.2 | 17896 | 4.8107 |
| 0.3 | 13748 | 3.6957 |
| 0.4 | 11178 | 3.0048 |
| 0.5 | 8795 | 2.3642 |
| 0.6 | 7740 | 2.0806 |
| 0.7 | 5917 | 1.5906 |
| 0.8 | 4647 | 1.2492 |
| 0.9 | 3616 | 0.9720 |
| Total | 372003 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 11905 | 3.2002 |
| 0.4 | 12235 | 3.2890 |
| 0.5 | 13559 | 3.6449 |
| 0.6 | 21169 | 5.6905 |
| 0.7 | 35938 | 9.6607 |
| 0.8 | 59715 | 16.0523 |
| 0.9 | 217232 | 58.3952 |
| 1.0 | 250 | 0.0672 |
| Total | 372003 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 157445 | 71.0742 |
| 0.1 | 15945 | 7.1979 |
| 0.2 | 10237 | 4.6212 |
| 0.3 | 9126 | 4.1197 |
| 0.4 | 7173 | 3.2381 |
| 0.5 | 5998 | 2.7076 |
| 0.6 | 4903 | 2.2133 |
| 0.7 | 4421 | 1.9957 |
| 0.8 | 4158 | 1.8770 |
| 0.9 | 2116 | 0.9552 |
| Total | 221522 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 7765 | 3.5053 |
| 0.4 | 7654 | 3.4552 |
| 0.5 | 9288 | 4.1928 |
| 0.6 | 13501 | 6.0947 |
| 0.7 | 23011 | 10.3877 |
| 0.8 | 35649 | 16.0928 |
| 0.9 | 124505 | 56.2043 |
| 1.0 | 149 | 0.0673 |
| Total | 221522 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 164388 | 73.0587 |
| 0.1 | 15978 | 7.1011 |
| 0.2 | 10946 | 4.8647 |
| 0.3 | 8064 | 3.5839 |
| 0.4 | 6905 | 3.0688 |
| 0.5 | 5398 | 2.3990 |
| 0.6 | 4619 | 2.0528 |
| 0.7 | 3834 | 1.7039 |
| 0.8 | 3020 | 1.3422 |
| 0.9 | 1856 | 0.8249 |
| Total | 225008 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 8245 | 3.6643 |
| 0.4 | 8170 | 3.6310 |
| 0.5 | 9527 | 4.2341 |
| 0.6 | 13858 | 6.1589 |
| 0.7 | 22678 | 10.0788 |
| 0.8 | 36471 | 16.2088 |
| 0.9 | 125827 | 55.9211 |
| 1.0 | 232 | 0.1031 |
| Total | 225008 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 427690 | 76.2569 |
| 0.1 | 34752 | 6.1963 |
| 0.2 | 22853 | 4.0747 |
| 0.3 | 18159 | 3.2377 |
| 0.4 | 13854 | 2.4702 |
| 0.5 | 11308 | 2.0162 |
| 0.6 | 10938 | 1.9502 |
| 0.7 | 9368 | 1.6703 |
| 0.8 | 6218 | 1.1087 |
| 0.9 | 5714 | 1.0188 |
| Total | 560854 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 21991 | 3.9210 |
| 0.4 | 22806 | 4.0663 |
| 0.5 | 28486 | 5.0790 |
| 0.6 | 43147 | 7.6931 |
| 0.7 | 64906 | 11.5727 |
| 0.8 | 94495 | 16.8484 |
| 0.9 | 284377 | 50.7043 |
| 1.0 | 646 | 0.1152 |
| Total | 560854 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering